Assays which are available in the network
Description: Reference for every available assay in network.
Properties
| Property | Description | Data Type |
|---|---|---|
| wes | Whole exome sequencing. |
<
array
>
|
| rna | RNA assay for expression analysis. |
<
array
>
|
| tcr | TCR sequencing assay. |
<
array
>
|
| cytof_10021 | Information about the acquisition and analysis CyTOF data for 10021 and similarly formatted trials. |
<
array
>
|
| cytof_e4412 | Information about the acquisition and analysis CyTOF data for E4412 and similarly formatted trials. |
<
array
>
|
| cytof_s1609_gd2car | Information about the acquisition and analysis CyTOF data for S1609 and similarly formatted trials. |
<
array
>
|
| elisa | Base information about the acquisition and analysis of ELISA data. |
<
array
>
|
| olink | High-throughput multiplexed assays for protein biomarker discovery. | assays.olink_assay |
| mif | Multiplex immunofluorescence. |
<
array
>
|
| micsss | Multiplexed immunohistochemical consecutive staining on single slide. |
<
array
>
|
| ihc | Immunohistochemical analysis. |
<
array
>
|
| hande | H & E. |
<
array
>
|
| nanostring | Nanostring |
<
array
>
|
available_assays.full.json
{
"$id": "available_assays",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Reference for every available assay in network.",
"mergeStrategy": "objectMerge",
"properties": {
"cytof_10021": {
"description": "Information about the acquisition and analysis CyTOF data for 10021 and similarly formatted trials.",
"items": {
"$id": "cytof_10021",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "cytof_core",
"$schema": "metaschema/strict_meta_schema.json#",
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"antibody": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"entry": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
}
},
"description": "Base information about the acquisition and analysis CyTOF data.",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "isotope"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"excluded_samples": {
"$id": "excluded_samples",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A list of samples excluded from analysis, along with the reasons why.",
"items": {
"additionalProperties": false,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"reason_excluded": {
"description": "A comment describing why this sample is missing from the pipeline output.",
"type": "string"
}
},
"required": [
"cimac_id",
"reason_excluded"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cytof_antibodies",
"assay_run_id",
"batch_id"
],
"title": "CYTOF Run",
"type": "object"
}
],
"description": "Information about the acquisition and analysis CyTOF data for 10021 and similarly formatted trials.",
"mergeStrategy": "objectMerge",
"properties": {
"acquisition_buffer": {
"description": "Cell staining buffer used for antibody and cell dilution.",
"type": "string"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"astrolabe_analysis": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"astrolabe_reports": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"bead_removal": {
"description": "Boolean to indicate whether beads have been removed after normalization process",
"type": "boolean"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "isotope"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"date_of_acquisition": {
"description": "Date of CyTOF batch acquisition.",
"type": "string"
},
"debarcoding_protocol": {
"description": "The strategy/kit used to barcode CyTOF samples, if any",
"type": "string"
},
"excluded_samples": {
"$id": "excluded_samples",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A list of samples excluded from analysis, along with the reasons why.",
"items": {
"additionalProperties": false,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"reason_excluded": {
"description": "A comment describing why this sample is missing from the pipeline output.",
"type": "string"
}
},
"required": [
"cimac_id",
"reason_excluded"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"harware_version": {
"description": "Version no. of instrument hardware used.",
"type": "string"
},
"injector": {
"description": "Name of Injector component used as part of the CyTOF software",
"type": "string"
},
"instrument": {
"description": "Name of CyTOF instrument on which experiment was conducted.",
"type": "string"
},
"normalization_method": {
"description": "Process used for normalization prior to analysis, if any.",
"enum": [
"Fluidigm",
"Other"
],
"type": "string"
},
"records": {
"description": "A single data record from CyTOF assay batch.",
"items": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"source_fcs": {
"items": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"type": "array"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"assay_creator",
"batch_id",
"records"
],
"title": "CYTOF Run",
"type": "object"
},
"mergeOptions": {
"idRef": "batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"cytof_e4412": {
"description": "Information about the acquisition and analysis CyTOF data for E4412 and similarly formatted trials.",
"items": {
"$id": "cytof_e4412",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "cytof_core",
"$schema": "metaschema/strict_meta_schema.json#",
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"antibody": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"entry": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
}
},
"description": "Base information about the acquisition and analysis CyTOF data.",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "isotope"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"excluded_samples": {
"$id": "excluded_samples",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A list of samples excluded from analysis, along with the reasons why.",
"items": {
"additionalProperties": false,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"reason_excluded": {
"description": "A comment describing why this sample is missing from the pipeline output.",
"type": "string"
}
},
"required": [
"cimac_id",
"reason_excluded"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cytof_antibodies",
"assay_run_id",
"batch_id"
],
"title": "CYTOF Run",
"type": "object"
}
],
"definitions": {
"participant": {
"additionalProperties": false,
"description": "A data record for a single participant from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_participant_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_participant_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_participant_id $ref.Id of a participant within this clinical trial, that this assay record is based upon.",
"description": "Participant identifier assigned by the CIMAC-CIDC Network. Formated as: C?????? (first 7 characters of CIMAC ID)",
"example": "CTTTP01",
"in_doc_ref_pattern": "/participants/*/cimac_participant_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}$",
"type": "string"
},
"control": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
}
},
"required": [
"input_files"
],
"type": "object"
},
"participant_debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cimac_participant_id",
"samples",
"control"
],
"type": "object"
}
},
"description": "Information about the acquisition and analysis CyTOF data for E4412 and similarly formatted trials.",
"mergeStrategy": "objectMerge",
"properties": {
"acquisition_buffer": {
"description": "Cell staining buffer used for antibody and cell dilution.",
"type": "string"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"astrolabe_analysis": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"astrolabe_reports": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "isotope"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"debarcoding_protocol": {
"description": "The strategy/kit used to barcode CyTOF samples, if any",
"type": "string"
},
"excluded_samples": {
"$id": "excluded_samples",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A list of samples excluded from analysis, along with the reasons why.",
"items": {
"additionalProperties": false,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"reason_excluded": {
"description": "A comment describing why this sample is missing from the pipeline output.",
"type": "string"
}
},
"required": [
"cimac_id",
"reason_excluded"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"participants": {
"items": {
"additionalProperties": false,
"description": "A data record for a single participant from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_participant_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_participant_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_participant_id $ref.Id of a participant within this clinical trial, that this assay record is based upon.",
"description": "Participant identifier assigned by the CIMAC-CIDC Network. Formated as: C?????? (first 7 characters of CIMAC ID)",
"example": "CTTTP01",
"in_doc_ref_pattern": "/participants/*/cimac_participant_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}$",
"type": "string"
},
"control": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
}
},
"required": [
"input_files"
],
"type": "object"
},
"participant_debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cimac_participant_id",
"samples",
"control"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_participant_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"source_fcs": {
"items": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"type": "array"
}
},
"required": [
"assay_creator",
"batch_id",
"participants"
],
"title": "CYTOF Run",
"type": "object"
},
"mergeOptions": {
"idRef": "batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"cytof_s1609_gd2car": {
"description": "Information about the acquisition and analysis CyTOF data for S1609 and similarly formatted trials.",
"items": {
"$id": "cytof_s1609_gd2car",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "cytof_core",
"$schema": "metaschema/strict_meta_schema.json#",
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"antibody": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"entry": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
}
},
"description": "Base information about the acquisition and analysis CyTOF data.",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "isotope"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"excluded_samples": {
"$id": "excluded_samples",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A list of samples excluded from analysis, along with the reasons why.",
"items": {
"additionalProperties": false,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"reason_excluded": {
"description": "A comment describing why this sample is missing from the pipeline output.",
"type": "string"
}
},
"required": [
"cimac_id",
"reason_excluded"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cytof_antibodies",
"assay_run_id",
"batch_id"
],
"title": "CYTOF Run",
"type": "object"
}
],
"description": "Information about the acquisition and analysis CyTOF data for S1609, GD2CAR and similarly formatted trials.",
"mergeStrategy": "objectMerge",
"properties": {
"acquisition_buffer": {
"description": "Cell staining buffer used for antibody and cell dilution.",
"type": "string"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"astrolabe_analysis": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"astrolabe_reports": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"bead_removal": {
"description": "Boolean to indicate whether beads have been removed after normalization process",
"type": "boolean"
},
"control_spike_in_fcs": {
"items": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"type": "array"
},
"controls_fcs": {
"items": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"type": "array"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Barcoding",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "isotope"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"date_of_acquisition": {
"description": "Date of CyTOF batch acquisition.",
"type": "string"
},
"debarcoding_protocol": {
"description": "The strategy/kit used to barcode CyTOF samples, if any",
"type": "string"
},
"harware_version": {
"description": "Version no. of instrument hardware used.",
"type": "string"
},
"injector": {
"description": "Name of Injector component used as part of the CyTOF software",
"type": "string"
},
"instrument": {
"description": "Name of CyTOF instrument on which experiment was conducted.",
"type": "string"
},
"normalization_method": {
"description": "Process used for normalization prior to analysis, if any.",
"enum": [
"Fluidigm",
"Other"
],
"type": "string"
},
"records": {
"description": "A single data record from CyTOF assay batch.",
"items": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"source_fcs": {
"items": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"type": "array"
}
},
"required": [
"assay_creator",
"batch_id",
"records"
],
"title": "CYTOF Run",
"type": "object"
},
"mergeOptions": {
"idRef": "batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"elisa": {
"description": "Base information about the acquisition and analysis of ELISA data.",
"items": {
"$id": "elisa_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"antigen": {
"additionalProperties": false,
"description": "Data specific to antigen preparation on the ELISA assay.",
"mergeStrategy": "objectMerge",
"properties": {
"antigen": {
"description": "Identifying name for the antigen.",
"type": "string"
},
"antigen_type": {
"description": "The type of antigen, either protein or peptide",
"enum": [
"protein",
"peptide"
],
"type": "string"
},
"final_concentration": {
"description": "The concentration of the antigen after dilution.",
"type": "number"
},
"final_concentration_units": {
"description": "The concentration units for the antigen after dilution.",
"enum": [
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Nanomolar",
"Micromolar",
"Millimolar",
"Not Reported",
"Other"
],
"type": "string"
}
},
"required": [
"antigen",
"antigen_type"
],
"type": "object"
}
},
"description": "High-throughput multiplexed assays for protein biomarker discovery.",
"mergeStrategy": "objectMerge",
"properties": {
"antigens": {
"items": {
"additionalProperties": false,
"description": "Data specific to antigen preparation on the ELISA assay.",
"mergeStrategy": "objectMerge",
"properties": {
"antigen": {
"description": "Identifying name for the antigen.",
"type": "string"
},
"antigen_type": {
"description": "The type of antigen, either protein or peptide",
"enum": [
"protein",
"peptide"
],
"type": "string"
},
"final_concentration": {
"description": "The concentration of the antigen after dilution.",
"type": "number"
},
"final_concentration_units": {
"description": "The concentration units for the antigen after dilution.",
"enum": [
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Nanomolar",
"Micromolar",
"Millimolar",
"Not Reported",
"Other"
],
"type": "string"
}
},
"required": [
"antigen",
"antigen_type"
],
"type": "object"
},
"mergeOptions": {
"idRef": "antigen"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run.",
"type": "string"
},
"assay_xlsx": {
"$comment": "TODO Maybe add array of antibodies parsing.",
"$id": "artifact_elisa_xlsx",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an ELISA file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ELISA",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ELISA results artifact",
"type": "object"
}
},
"required": [
"assay_run_id",
"assay_xlsx",
"antigens"
],
"title": "ELISA Assay",
"type": "object"
},
"mergeOptions": {
"idRef": "assay_run_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"hande": {
"description": "H & E.",
"items": {
"$id": "hande_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"input": {
"additionalProperties": false,
"description": "H & E assay input files.",
"properties": {
"image_file": {
"$comment": "Path to the H & E image in SVS format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"image_file"
],
"type": "object"
},
"record": {
"additionalProperties": false,
"description": "A single data record from H & E assay.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"comment": {
"description": "A text comment regarding this slide.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "H & E assay input files.",
"properties": {
"image_file": {
"$comment": "Path to the H & E image in SVS format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"image_file"
],
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"type": "object"
}
},
"description": "H & E assay",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"records": {
"description": "A single data record from H & E assay.",
"items": {
"additionalProperties": false,
"description": "A single data record from H & E assay.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"comment": {
"description": "A text comment regarding this slide.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "H & E assay input files.",
"properties": {
"image_file": {
"$comment": "Path to the H & E image in SVS format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"image_file"
],
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"records",
"assay_creator"
],
"title": "H&E Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"ihc": {
"description": "Immunohistochemical analysis.",
"items": {
"$id": "ihc",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"ihc_antibody": {
"additionalProperties": false,
"allOf": [
{
"$id": "antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common information about an antibody used in a number of immune-oncology assays.",
"inheritableBase": true,
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"antibody"
],
"title": "Antibody",
"type": "object"
}
],
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio for antibody dilution.",
"type": "string"
},
"incubation_temp": {
"description": "Temperature used for antibody incubation.",
"type": "string"
},
"incubation_time": {
"description": "Time duration of antibody incubation.",
"format": "time",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"dilution",
"incubation_time",
"incubation_temp"
],
"type": "object"
},
"record": {
"additionalProperties": false,
"anyOf": [
{
"required": [
"tumor_proportion_score"
]
},
{
"required": [
"combined_positive_score"
]
},
{
"required": [
"inflammatory_cells"
]
},
{
"required": [
"positive_inflammatory_cell_area"
]
},
{
"required": [
"intensity"
]
},
{
"required": [
"percentage_expression"
]
},
{
"required": [
"h_score"
]
}
],
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"combined_positive_score": {
"description": "Combined Positive Score (CPS) is the percentage of marker staining cells (tumor cells and cells that are non-tumor) relative to all viable tumor cells. (0-1)",
"type": [
"number",
"string"
]
},
"comment": {
"description": "A text comment regarding this slide.",
"type": "string"
},
"files": {
"additionalProperties": false,
"properties": {
"ihc_image": {
"$comment": "Path to IHC image in TIFF format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"ihc_image"
],
"type": "object"
},
"h_score": {
"description": "A summation of the percentage of area stained at each intensity level multiplied by the weighted intensity. (0-300)",
"type": [
"integer",
"string"
]
},
"inflammatory_cells": {
"description": "Percentage of inflammatory cells (non-tumor cells) showing marker staining relative to all inflammatory cells. (0-1)",
"type": [
"number",
"string"
]
},
"intensity": {
"description": "A measure of the intensity or brightness of the protein. (0-3)",
"type": [
"number",
"string"
]
},
"marker_positive": {
"description": "Indicates whether the marker is considered positive by clinical trial guidelines (if applicable).",
"enum": [
"positive",
"negative",
"no_call"
],
"type": "string"
},
"percentage_expression": {
"description": "A percentage of the relevant cells considered positive. (0-100)",
"type": [
"number",
"string"
]
},
"positive_inflammatory_cell_area": {
"description": "Area of PD-L1+ Inflammatory Cells over the area of TSI + IT as a percentage. (0-1)",
"type": [
"number",
"string"
]
},
"tumor_proportion_score": {
"description": "Tumor Proportion Score (TPS) is the percentage of viable tumor cells showing marker staining relative to all viable tumor cells. (0-1)",
"type": [
"number",
"string"
]
}
},
"required": [
"cimac_id",
"files",
"marker_positive"
],
"type": "object"
}
},
"description": "Immunohistochemical analysis.",
"mergeStrategy": "objectMerge",
"properties": {
"antibody": {
"additionalProperties": false,
"allOf": [
{
"$id": "antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common information about an antibody used in a number of immune-oncology assays.",
"inheritableBase": true,
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"antibody"
],
"title": "Antibody",
"type": "object"
}
],
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio for antibody dilution.",
"type": "string"
},
"incubation_temp": {
"description": "Temperature used for antibody incubation.",
"type": "string"
},
"incubation_time": {
"description": "Time duration of antibody incubation.",
"format": "time",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"dilution",
"incubation_time",
"incubation_temp"
],
"type": "object"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"autostainer_model": {
"description": "Model version of the autostainer instrument.",
"enum": [
"Bond RX",
"Bond MAX",
"Other",
"N/A"
],
"type": "string"
},
"records": {
"description": "A single data record from IHC assay.",
"items": {
"additionalProperties": false,
"anyOf": [
{
"required": [
"tumor_proportion_score"
]
},
{
"required": [
"combined_positive_score"
]
},
{
"required": [
"inflammatory_cells"
]
},
{
"required": [
"positive_inflammatory_cell_area"
]
},
{
"required": [
"intensity"
]
},
{
"required": [
"percentage_expression"
]
},
{
"required": [
"h_score"
]
}
],
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"combined_positive_score": {
"description": "Combined Positive Score (CPS) is the percentage of marker staining cells (tumor cells and cells that are non-tumor) relative to all viable tumor cells. (0-1)",
"type": [
"number",
"string"
]
},
"comment": {
"description": "A text comment regarding this slide.",
"type": "string"
},
"files": {
"additionalProperties": false,
"properties": {
"ihc_image": {
"$comment": "Path to IHC image in TIFF format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"ihc_image"
],
"type": "object"
},
"h_score": {
"description": "A summation of the percentage of area stained at each intensity level multiplied by the weighted intensity. (0-300)",
"type": [
"integer",
"string"
]
},
"inflammatory_cells": {
"description": "Percentage of inflammatory cells (non-tumor cells) showing marker staining relative to all inflammatory cells. (0-1)",
"type": [
"number",
"string"
]
},
"intensity": {
"description": "A measure of the intensity or brightness of the protein. (0-3)",
"type": [
"number",
"string"
]
},
"marker_positive": {
"description": "Indicates whether the marker is considered positive by clinical trial guidelines (if applicable).",
"enum": [
"positive",
"negative",
"no_call"
],
"type": "string"
},
"percentage_expression": {
"description": "A percentage of the relevant cells considered positive. (0-100)",
"type": [
"number",
"string"
]
},
"positive_inflammatory_cell_area": {
"description": "Area of PD-L1+ Inflammatory Cells over the area of TSI + IT as a percentage. (0-1)",
"type": [
"number",
"string"
]
},
"tumor_proportion_score": {
"description": "Tumor Proportion Score (TPS) is the percentage of viable tumor cells showing marker staining relative to all viable tumor cells. (0-1)",
"type": [
"number",
"string"
]
}
},
"required": [
"cimac_id",
"files",
"marker_positive"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu",
"AT2 Turbo"
],
"type": "string"
},
"staining_platform": {
"description": "Staining platform used for tissue sample labeling.",
"enum": [
"auto",
"manual"
],
"type": "string"
}
},
"required": [
"slide_scanner_model",
"staining_platform",
"autostainer_model",
"antibody",
"records"
],
"title": "IHC Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"micsss": {
"description": "Multiplexed immunohistochemical consecutive staining on single slide.",
"items": {
"$id": "micsss",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Base information about the acquisition and analysis of a quantitative pathology image.",
"inheritableBase": true,
"properties": {
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
}
},
"required": [
"slide_scanner_model"
],
"title": "Image",
"type": "object"
},
{
"$id": "imaging_data",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Shared schema for experiments involving the use of imaging data.",
"inheritableBase": true,
"properties": {
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"staining": {
"description": "'manual' or Model version of the autostainer instrument used for tissue sample labeling.",
"enum": [
"manual",
"Bond RX"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"title": "Imaging Data",
"type": "object"
}
],
"description": "Multiplexed immunohistochemical consecutive staining on single slide.",
"properties": {
"antibody": {
"items": {
"$id": "micsss_antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common information about an antibody used in a number of immune-oncology assays.",
"inheritableBase": true,
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"antibody"
],
"title": "Antibody",
"type": "object"
}
],
"description": "Data specific to antibody preparation on the multiplex immunohistochemical platform.",
"properties": {
"ar_incubation_time": {
"description": "Time of AR reagent incubation.",
"format": "time",
"type": "string"
},
"ar_ph": {
"description": "pH levels of reagents from heating antigen retrieval procedure.",
"type": "string"
},
"ar_reagent": {
"description": "Heating antigen retrieval reagents for tissue preparation.",
"type": "string"
},
"isotype": {
"description": "Antibody isotype used to help differentiate non-specific background signal from specific antibody signal.",
"type": "string"
},
"postPrimary_linker_block": {
"description": "Linker block between the antibody and the therapeutic drug.",
"type": "string"
},
"primary_antibody_block": {
"description": "Blocking reagent used for primary antibody sample.",
"type": "string"
},
"primary_antibody_dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"primary_antibody_incubation_temp": {
"description": "Temperature used for primary antibody incubation.",
"type": "string"
},
"primary_antibody_incubation_time": {
"description": "Time of primary antibody incubation.",
"format": "time",
"type": "string"
},
"secondary_antibody": {
"description": "Secondary antibody used to bind to primary antibody for detection assistance.",
"type": "string"
},
"secondary_antibody_block": {
"description": "Secondary antibody blocking reagent used for primary sample.",
"type": "string"
},
"secondary_antibody_dilution": {
"description": "Concentration ratio of dilution buffer for secondary antibody prep.",
"type": "string"
},
"secondary_antibody_incubation_time": {
"description": "Temperature used for secondary antibody incubation.",
"format": "time",
"type": "string"
},
"secondary_cat_num": {
"description": "Antibody registry catalog number assigned to secondary antibody sample.",
"type": "number"
},
"secondary_company": {
"description": "Company from which secondary antibody sample was derived.",
"type": "string"
},
"secondary_lot_num": {
"description": "Identification number assigned to the particular quantity or lot of secondary antibody material from manufacturer.",
"type": "number"
},
"species": {
"description": "Host species from which primary antibody sample was derived.",
"type": "string"
}
},
"required": [
"primary_antibody_block"
],
"title": "MICSSS antibody",
"type": "object"
},
"type": "array"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"records": {
"description": "A single data record from micsss assay.",
"items": {
"$id": "micsss_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "A single data record from micsss assay.",
"properties": {
"files": {
"$id": "micsss_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "micsss assay input files.",
"properties": {
"Composite Image Artifacts": {
"description": "Regions of interest obtained from composite images.",
"items": {
"$id": "composite_image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from composite images.",
"inheritableBase": true,
"properties": {
"component_data": {
"$comment": "Imaging data resulting from the individual components of the imaging experiment.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"composite_image": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"im3": {
"$comment": "PerkinElmer Multispectral Images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"title": "Composite Image",
"type": "object"
},
"type": "array"
},
"Mapping Artifacts": {
"description": "Regions of interest obtained from image mapping.",
"items": {
"$id": "image_mapping",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from image mapping.",
"inheritableBase": true,
"properties": {
"binary_seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped with binary values.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"cell_seg_data": {
"$comment": "Data produced from the analysis of cellular image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"cell_seg_data_summary": {
"$comment": "Summary of the results of a cell segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"score_data": {
"items": {
"$comment": "Generation of values based on experiment data.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"type": "array"
},
"seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"tissue_seg_data": {
"$comment": "Data produced from the analysis of tissue image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"tissue_seg_data_summary": {
"$comment": "Summary of the results of a tissue segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"title": "Image Mapping",
"type": "object"
},
"type": "array"
},
"micsss_output_summary": {
"$comment": "Summary of the results of the experiment.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [],
"title": "Multiplexed Immunohistochemical Input Files",
"type": "object"
},
"micsss_exported_data_folder": {
"description": "Folder path containing imaging files.",
"type": "string"
},
"project_qupath_folder": {
"description": "Folder path containing files produced from a QuPath image analysis.",
"type": "string"
}
},
"required": [
"project_qupath_folder",
"micsss_exported_data_folder"
],
"title": "micsss assay record",
"type": "object"
},
"type": "array"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"required": [
"records"
],
"title": "MICSSS Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"mif": {
"description": "Multiplex immunofluorescence.",
"items": {
"$id": "mif",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Base information about the acquisition and analysis of a quantitative pathology image.",
"inheritableBase": true,
"properties": {
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
}
},
"required": [
"slide_scanner_model"
],
"title": "Image",
"type": "object"
},
{
"$id": "imaging_data",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Shared schema for experiments involving the use of imaging data.",
"inheritableBase": true,
"properties": {
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"staining": {
"description": "'manual' or Model version of the autostainer instrument used for tissue sample labeling.",
"enum": [
"manual",
"Bond RX"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"title": "Imaging Data",
"type": "object"
}
],
"description": "Multiplex immunofluorescence.",
"mergeStrategy": "objectMerge",
"properties": {
"antibodies": {
"items": {
"$id": "mif_antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common information about an antibody used in a number of immune-oncology assays.",
"inheritableBase": true,
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"antibody"
],
"title": "Antibody",
"type": "object"
}
],
"description": "Data specific to antibody preparation on the multiplex immunofluorescence platform.",
"mergeStrategy": "objectMerge",
"properties": {
"amplification_time": {
"description": "Length of time required for amplified signal detection.",
"format": "time",
"type": "string"
},
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"antigen_retrieval_time": {
"description": "Length of time needed for antigen retrieval.",
"format": "time",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilutent": {
"description": "Dilution agent used for antibody sample.",
"type": "string"
},
"export_name": {
"description": "Name of this antibody in InForm export, e.g. 'CD8 (Opal 520)'",
"type": "string"
},
"fluor_dilution": {
"description": "Concentration ratio for fluor dilution agent.",
"type": "string"
},
"fluor_wavelength": {
"description": "Wavelength registered for Alexa Fluor processing.",
"type": "integer"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"primary_ab_dilution": {
"description": "Concentration ratio for primary antibody dilution.",
"type": "string"
},
"primary_incubation_time": {
"description": "Length of time for primary antibody incubation.",
"format": "time",
"type": "string"
},
"staining_order": {
"description": "Order of staining applied",
"type": "integer"
}
},
"required": [
"fluor_wavelength",
"primary_ab_dilution",
"dilutent",
"fluor_dilution",
"antigen_retrieval_time",
"primary_incubation_time",
"amplification_time"
],
"title": "mIF antibody",
"type": "object"
},
"mergeOptions": {
"idRef": "antibody"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"panel": {
"enum": [
"Panel 1: PD-L1, CD68, PD-1, CD8, CD3, pan-cytokeratin, DAPI",
"Panel 2: FOXP3, Granzyme B, CD45RO, CD8, CD3, pan-cytokeratin, DAPI",
"Panel 3: pan-cytokeratin, CD8, PD-1, PD-L1, DAPI",
"Panel 4: SOX10, CD8, PD-1, PD-L1, DAPI"
],
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"records": {
"description": "A single data record from mIF assay.",
"items": {
"$id": "mif_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "A single data record from mIF assay.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$id": "mif_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "mIF assay input files.",
"properties": {
"mif_output_summary": {
"$comment": "Summary of the results of the experiment.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"regions_of_interest": {
"items": {
"$id": "mif_roi",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "composite_image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from composite images.",
"inheritableBase": true,
"properties": {
"component_data": {
"$comment": "Imaging data resulting from the individual components of the imaging experiment.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"composite_image": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"im3": {
"$comment": "PerkinElmer Multispectral Images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"title": "Composite Image",
"type": "object"
}
],
"description": "A region of interest (ROI) is a portion of an image which has been analyzed using image processing software.",
"mergeStrategy": "objectMerge",
"properties": {
"component_data": {
"$comment": "Imaging data resulting from the individual components of the imaging experiment.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"composite_image": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"exports": {
"items": {
"$id": "mif_export",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "image_mapping",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from image mapping.",
"inheritableBase": true,
"properties": {
"binary_seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped with binary values.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"cell_seg_data": {
"$comment": "Data produced from the analysis of cellular image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"cell_seg_data_summary": {
"$comment": "Summary of the results of a cell segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"score_data": {
"items": {
"$comment": "Generation of values based on experiment data.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"type": "array"
},
"seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"tissue_seg_data": {
"$comment": "Data produced from the analysis of tissue image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"tissue_seg_data_summary": {
"$comment": "Summary of the results of a tissue segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"title": "Image Mapping",
"type": "object"
}
],
"description": "An analysis export from inForm of a region of interest (ROI).",
"mergeOptions": {
"idRef": "/export_id"
},
"mergeStrategy": "objectMerge",
"properties": {
"binary_seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped with binary values.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"cell_seg_data": {
"$comment": "Data produced from the analysis of cellular image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"cell_seg_data_summary": {
"$comment": "Summary of the results of a cell segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"export_id": {
"description": "Name used for an inForm export of a region of interest within one mIF slide, e.g. CD8, CD45RO",
"type": "string"
},
"image_with_all_seg": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"image_with_cell_seg_map": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"image_with_phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"image_with_tissue_seg": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"score_data": {
"items": {
"$comment": "Generation of values based on experiment data.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"type": "array"
},
"tissue_seg_data": {
"$comment": "Data produced from the analysis of tissue image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"tissue_seg_data_summary": {
"$comment": "Summary of the results of a tissue segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"export_id",
"cell_seg_data",
"cell_seg_data_summary"
]
},
"mergeOptions": {
"idRef": "/export_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"im3": {
"$comment": "PerkinElmer Multispectral Images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"roi_id": {
"description": "Identifier of a region of interest within one mIF slide, e.g. 1, 2, 3 or [123 x 321]",
"type": "string"
}
},
"required": [
"roi_id",
"exports"
]
},
"mergeOptions": {
"idRef": "/roi_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"roi_annotations": {
"$comment": "Text describing region of interest for experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"whole_slide_imaging_file": {
"$comment": "Digital slide produced from the scanning of conventional glass slides.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"regions_of_interest"
],
"title": "Multiplex Immunofluorescence Input Files",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "mIF assay record",
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
},
"staining": {
"description": "'manual' or Model version of the autostainer instrument used for tissue sample labeling.",
"enum": [
"manual",
"Bond RX"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"required": [
"records",
"panel",
"antibodies"
],
"title": "mIF Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"nanostring": {
"description": "Nanostring",
"items": {
"$id": "nanostring_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"run": {
"additionalProperties": false,
"description": "A single Nanostring run.",
"properties": {
"control_raw_rcc": {
"$comment": "The RCC data file for a reference RNA sample",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
},
"run_id": {
"description": "A unique ID that separates the different runs of the given same sample.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A data record for a single sample from a single Nanostring run.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"raw_rcc": {
"$comment": "The RCC data file generated by Nanostring for the given sample in the given run.",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
}
},
"required": [
"cimac_id",
"raw_rcc"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"run_id",
"samples"
],
"type": "object"
},
"sample": {
"additionalProperties": false,
"description": "A data record for a single sample from a single Nanostring run.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"raw_rcc": {
"$comment": "The RCC data file generated by Nanostring for the given sample in the given run.",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
}
},
"required": [
"cimac_id",
"raw_rcc"
],
"type": "object"
}
},
"description": "A microarray assay for expression levels, suitable for smaller samples than RNA-seq",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"batch_id": {
"description": "A unique ID that separates the different batches of Nanostring.",
"type": "string"
},
"data": {
"additionalProperties": false,
"properties": {
"normalized": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"raw": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"runs": {
"items": {
"additionalProperties": false,
"description": "A single Nanostring run.",
"properties": {
"control_raw_rcc": {
"$comment": "The RCC data file for a reference RNA sample",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
},
"run_id": {
"description": "A unique ID that separates the different runs of the given same sample.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A data record for a single sample from a single Nanostring run.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"raw_rcc": {
"$comment": "The RCC data file generated by Nanostring for the given sample in the given run.",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
}
},
"required": [
"cimac_id",
"raw_rcc"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"run_id",
"samples"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/run_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"data",
"runs"
],
"title": "Nanostring Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"olink": {
"$comment": "NB This is not array as every other assay. Will update data on any olink upload.",
"$id": "olink_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"batch": {
"additionalProperties": false,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_panel_lot": {
"description": "Lot number of the assay panel.",
"type": "string"
},
"batch_id": {
"description": "A unique identifier for this Olink upload",
"type": "string"
},
"combined": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
},
"panel": {
"description": "Panel used for the assay.",
"type": "string"
},
"records": {
"description": "A single data record from Olink assay.",
"items": {
"additionalProperties": false,
"description": "A single data record from Olink assay.",
"properties": {
"baseline_correction": {
"description": "Method used for baseline correction.",
"type": "string"
},
"chip_barcode": {
"description": "Chip barcode number.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"fludigm_application_build": {
"description": "Build of the Fluidgm application used.",
"type": "string"
},
"fludigm_application_version": {
"description": "Version of the Fluidgm application used.",
"type": "string"
},
"instrument": {
"description": "Instrument used for the Olink assay.",
"type": "string"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples analyzed in the assay.",
"type": "number"
},
"number_of_samples_failed": {
"description": "Number of samples failed in the assay.",
"type": "number"
},
"passive_reference": {
"description": "Passive Reference.",
"type": "string"
},
"probe_type": {
"description": "Probe Type.",
"type": "string"
},
"quality_threshold": {
"description": "Threshold used for quality cutoff.",
"type": "number"
},
"run_date": {
"description": "Date when the Olink assay was run.",
"format": "date",
"type": "string"
},
"run_time": {
"description": "Time when the Olink assay was run.",
"format": "time",
"type": "string"
}
},
"required": [
"number_of_samples",
"npx_manager_version",
"files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/chip_barcode"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"batch_id",
"panel",
"records",
"assay_creator"
],
"type": "object"
},
"combined_npx": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
},
"input": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"record": {
"additionalProperties": false,
"description": "A single data record from Olink assay.",
"properties": {
"baseline_correction": {
"description": "Method used for baseline correction.",
"type": "string"
},
"chip_barcode": {
"description": "Chip barcode number.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"fludigm_application_build": {
"description": "Build of the Fluidgm application used.",
"type": "string"
},
"fludigm_application_version": {
"description": "Version of the Fluidgm application used.",
"type": "string"
},
"instrument": {
"description": "Instrument used for the Olink assay.",
"type": "string"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples analyzed in the assay.",
"type": "number"
},
"number_of_samples_failed": {
"description": "Number of samples failed in the assay.",
"type": "number"
},
"passive_reference": {
"description": "Passive Reference.",
"type": "string"
},
"probe_type": {
"description": "Probe Type.",
"type": "string"
},
"quality_threshold": {
"description": "Threshold used for quality cutoff.",
"type": "number"
},
"run_date": {
"description": "Date when the Olink assay was run.",
"format": "date",
"type": "string"
},
"run_time": {
"description": "Time when the Olink assay was run.",
"format": "time",
"type": "string"
}
},
"required": [
"number_of_samples",
"npx_manager_version",
"files"
],
"type": "object"
}
},
"description": "High-throughput multiplexed assays for protein biomarker discovery.",
"mergeStrategy": "objectMerge",
"properties": {
"batches": {
"items": {
"additionalProperties": false,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_panel_lot": {
"description": "Lot number of the assay panel.",
"type": "string"
},
"batch_id": {
"description": "A unique identifier for this Olink upload",
"type": "string"
},
"combined": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
},
"panel": {
"description": "Panel used for the assay.",
"type": "string"
},
"records": {
"description": "A single data record from Olink assay.",
"items": {
"additionalProperties": false,
"description": "A single data record from Olink assay.",
"properties": {
"baseline_correction": {
"description": "Method used for baseline correction.",
"type": "string"
},
"chip_barcode": {
"description": "Chip barcode number.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"fludigm_application_build": {
"description": "Build of the Fluidgm application used.",
"type": "string"
},
"fludigm_application_version": {
"description": "Version of the Fluidgm application used.",
"type": "string"
},
"instrument": {
"description": "Instrument used for the Olink assay.",
"type": "string"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples analyzed in the assay.",
"type": "number"
},
"number_of_samples_failed": {
"description": "Number of samples failed in the assay.",
"type": "number"
},
"passive_reference": {
"description": "Passive Reference.",
"type": "string"
},
"probe_type": {
"description": "Probe Type.",
"type": "string"
},
"quality_threshold": {
"description": "Threshold used for quality cutoff.",
"type": "number"
},
"run_date": {
"description": "Date when the Olink assay was run.",
"format": "date",
"type": "string"
},
"run_time": {
"description": "Time when the Olink assay was run.",
"format": "time",
"type": "string"
}
},
"required": [
"number_of_samples",
"npx_manager_version",
"files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/chip_barcode"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"batch_id",
"panel",
"records",
"assay_creator"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"study": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
}
},
"required": [
"batches"
],
"title": "Olink Assay",
"type": "object"
},
"rna": {
"description": "RNA assay for expression analysis.",
"items": {
"$id": "rna_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"$id": "rna_assay-v0",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "ngs_assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common properties for NGS Assays.",
"inheritableBase": true,
"properties": {
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"sequencer_platform"
],
"title": "NGS Assay Core",
"type": "object"
}
],
"description": "Additional properties to describe a RNA assay for expression analysis.",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"enrichment_method": {
"description": "Method used for enriching for mRNA.",
"enum": [
"PolyA capture",
"Transcriptome capture v1",
"Ribo minus"
],
"type": "string"
},
"enrichment_vendor_kit": {
"description": "Vendor for the bait set used for enrichment, e.g. Twist, Agilent, IDT.",
"enum": [
"Agilent",
"Twist",
"IDT",
"NEB",
"Illumina - TruSeq Stranded PolyA mRNA",
"Illumina - TruSeq Stranded mRNA Sample Prep Kit",
"Illumina- TruSeq RNA Access Library Prep Kit"
],
"type": "string"
},
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"records": {
"description": "A single data record from RNAseq assay.",
"items": {
"additionalProperties": false,
"allOf": [
{
"$id": "ngs_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A single data record from an NGS assay.",
"inheritableBase": true,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "NGS assay record",
"type": "object"
}
],
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"dv200": {
"description": "The percentage of fragments > 200 nucleotides.",
"maximum": 1,
"minimum": 0,
"type": "number"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
},
"library_yield_ng": {
"description": "Resulting yield (in ng) from library construction.",
"type": "number"
},
"quality_flag": {
"description": "Flag used for quality.",
"type": "number"
},
"rin": {
"description": "RNA integrity number. (0-10)",
"maximum": 10,
"minimum": 0,
"type": "number"
},
"rqs": {
"description": "RNA quality score. (0-10)",
"maximum": 10,
"minimum": 0,
"type": "number"
}
},
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"enrichment_method",
"records"
],
"title": "RNA Gene Expression Assay version 0",
"type": "object"
}
],
"description": "An RNA assay for expression analysis.",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"title": "RNA Gene Expression Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"tcr": {
"description": "TCR sequencing assay.",
"items": {
"$id": "tcr_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "ngs_assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common properties for NGS Assays.",
"inheritableBase": true,
"properties": {
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"sequencer_platform"
],
"title": "NGS Assay Core",
"type": "object"
}
],
"description": "Additional properties to describe a TCR assay for expression analysis.",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"batch_id": {
"description": "TCRseq batch identification number.",
"type": "string"
},
"records": {
"description": "A single data record from TCRseq assay.",
"items": {
"$id": "tcr_entry",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "A single data record from TCRseq assay.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$id": "tcr_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "TCRseq assay input files.",
"properties": {
"replicates": {
"items": {
"$id": "tcr_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "reads_with_index",
"$schema": "metaschema/strict_meta_schema.json#",
"allOf": [
{
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
}
],
"description": "Index files associated with read files, in fastq.gz format",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"i1": {
"items": {
"$comment": "Fastq file for the first index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"i2": {
"items": {
"$comment": "Fastq file for the second index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"required": [
"i1",
"i2"
],
"title": "Reads with index",
"type": "object"
}
],
"description": "TCRseq replicate of interest.",
"mergeStrategy": "objectMerge",
"properties": {
"i1": {
"items": {
"$comment": "Fastq file for the first index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"i2": {
"items": {
"$comment": "Fastq file for the second index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"replicate_id": {
"description": "Replicate identifier.",
"type": "string"
},
"rna_quantity_ng": {
"description": "RNA quantity (in ng).",
"type": "number"
}
},
"required": [
"replicate_id"
]
},
"mergeOptions": {
"idRef": "/replicate_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"title": "TCRseq assay Input Files",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "TCRseq assay record",
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"sample_sheet": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
},
"sequencing_run_date": {
"description": "Date when the TCR sequencing was run.",
"format": "date",
"type": "string"
}
},
"required": [
"records",
"batch_id",
"sequencing_run_date",
"sample_sheet"
],
"title": "TCR Assay",
"type": "object"
},
"mergeOptions": {
"idRef": "batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"wes": {
"description": "Whole exome sequencing.",
"items": {
"$id": "wes_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "ngs_assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common properties for NGS Assays.",
"inheritableBase": true,
"properties": {
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"sequencer_platform"
],
"title": "NGS Assay Core",
"type": "object"
}
],
"definitions": {
"entry": {
"additionalProperties": false,
"allOf": [
{
"$id": "ngs_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A single data record from an NGS assay.",
"inheritableBase": true,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "NGS assay record",
"type": "object"
}
],
"description": "A single data record from WES assay.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
},
"output_files": {
"additionalProperties": false,
"description": "Sample wise analysis files for the WES assay.",
"properties": {
"alignment": {
"additionalProperties": false,
"description": "WES output align files.",
"properties": {
"align_recalibrated": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_recalibrated_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
},
"align_sorted_dedup": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_sorted_dedup_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
}
},
"required": [
"align_sorted_dedup",
"align_sorted_dedup_index"
],
"type": "object"
},
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"germline": {
"additionalProperties": false,
"description": "Germline variant output sample files.",
"oneOf": [
{
"required": [
"vcf_compare"
]
},
{
"required": [
"haplotyper_targets"
]
}
],
"properties": {
"haplotyper_targets": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
},
"vcf_compare": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"type": "object"
},
"metrics": {
"additionalProperties": false,
"description": "Coverage metrics output files.",
"properties": {
"all_summaries": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_broad": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mda": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mocha": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"coverage_metrics",
"target_metrics"
],
"type": "object"
},
"optitype": {
"additionalProperties": false,
"description": "HLA output files.",
"properties": {
"optitype_result": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"xhla_report_hla": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
}
},
"required": [
"optitype_result"
],
"type": "object"
}
},
"required": [
"cimac_id"
],
"type": "object"
},
"quality_flag": {
"description": "Flag used for quality.",
"type": "number"
},
"sequencing_date": {
"description": "Date of sequencing.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id"
],
"type": "object"
},
"sample_analysis": {
"additionalProperties": false,
"description": "Sample wise analysis files for the WES assay.",
"properties": {
"alignment": {
"additionalProperties": false,
"description": "WES output align files.",
"properties": {
"align_recalibrated": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_recalibrated_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
},
"align_sorted_dedup": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_sorted_dedup_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
}
},
"required": [
"align_sorted_dedup",
"align_sorted_dedup_index"
],
"type": "object"
},
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"germline": {
"additionalProperties": false,
"description": "Germline variant output sample files.",
"oneOf": [
{
"required": [
"vcf_compare"
]
},
{
"required": [
"haplotyper_targets"
]
}
],
"properties": {
"haplotyper_targets": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
},
"vcf_compare": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"type": "object"
},
"metrics": {
"additionalProperties": false,
"description": "Coverage metrics output files.",
"properties": {
"all_summaries": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_broad": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mda": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mocha": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"coverage_metrics",
"target_metrics"
],
"type": "object"
},
"optitype": {
"additionalProperties": false,
"description": "HLA output files.",
"properties": {
"optitype_result": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"xhla_report_hla": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
}
},
"required": [
"optitype_result"
],
"type": "object"
}
},
"required": [
"cimac_id"
],
"type": "object"
}
},
"description": "Whole exome sequencing.",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"bait_set": {
"description": "Bait set ID.",
"enum": [
"whole_exome_illumina_coding_v1",
"broad_custom_exome_v1",
"TWIST Dana Farber Custom Panel"
],
"type": "string"
},
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"read_length": {
"description": "Number of cycles for each sequencing read.",
"exclusiveMinimum": 0,
"maximum": 1000,
"type": "integer"
},
"records": {
"description": "A single data record from WES assay.",
"items": {
"additionalProperties": false,
"allOf": [
{
"$id": "ngs_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A single data record from an NGS assay.",
"inheritableBase": true,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "NGS assay record",
"type": "object"
}
],
"description": "A single data record from WES assay.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"mergeStrategy": "append",
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
},
"output_files": {
"additionalProperties": false,
"description": "Sample wise analysis files for the WES assay.",
"properties": {
"alignment": {
"additionalProperties": false,
"description": "WES output align files.",
"properties": {
"align_recalibrated": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_recalibrated_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
},
"align_sorted_dedup": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_sorted_dedup_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
}
},
"required": [
"align_sorted_dedup",
"align_sorted_dedup_index"
],
"type": "object"
},
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"germline": {
"additionalProperties": false,
"description": "Germline variant output sample files.",
"oneOf": [
{
"required": [
"vcf_compare"
]
},
{
"required": [
"haplotyper_targets"
]
}
],
"properties": {
"haplotyper_targets": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
},
"vcf_compare": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"type": "object"
},
"metrics": {
"additionalProperties": false,
"description": "Coverage metrics output files.",
"properties": {
"all_summaries": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_broad": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mda": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mocha": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"coverage_metrics",
"target_metrics"
],
"type": "object"
},
"optitype": {
"additionalProperties": false,
"description": "HLA output files.",
"properties": {
"optitype_result": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"xhla_report_hla": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
}
},
"required": [
"optitype_result"
],
"type": "object"
}
},
"required": [
"cimac_id"
],
"type": "object"
},
"quality_flag": {
"description": "Flag used for quality.",
"type": "number"
},
"sequencing_date": {
"description": "Date of sequencing.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
},
"sequencing_protocol": {
"description": "Protocol and version used for the sequencing.",
"enum": [
"Express Somatic Human WES (Deep Coverage) v1.1",
"Somatic Human WES v6"
],
"type": "string"
}
},
"required": [
"records",
"bait_set",
"read_length"
],
"title": "Whole Exome Sequencing Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
}
},
"title": "Assays which are available in the network",
"type": "object"
}